Evolutionary Bioinformatics

DNA Barcodes of Arabian Partridge and Philby's Rock Partridge: Implications for Phylogeny and Species Identification
Haseeb Ahmad Khan, Ibrahim Abdulwahid Arif and Mohammad Shobrak
Evolutionary Bioinformatics 2010:6 151-158
Original Research | Published on 05 Dec 2010

Computational Identification of Anthocyanin-Specific Transcription Factors using a Rice Microarray and Maximum Boundary Range Algorithm
Chang Kug Kim, Shoshi Kikuchi, Jang Ho Hahn, Soo Chul Park, Yong Hwan Kim and Byun Woo Lee
Evolutionary Bioinformatics 2010:6 133-141
Original Research | Published on 20 Oct 2010

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics
Michael S. Barker, Katrina M. Dlugosch, Louie Dinh, R. Sashikiran Challa, Nolan C. Kane, Matthew G. King and Loren H. Rieseberg
Evolutionary Bioinformatics 2010:6 143-149
Short Report | Published on 20 Oct 2010

Identifying the Combinatorial Effects of Histone Modifications by Association Rule Mining in Yeast
Jiang Wang, Xianhua Dai, Qian Xiang, Yangyang Deng, Jihua Feng, Zhiming Dai and Caisheng He
Evolutionary Bioinformatics 2010:6 113-131
Original Research | Published on 20 Sep 2010

A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA
Markus Göker, Guido W. Grimm, Alexander F. Auch, Ralf Aurahs and Michal Kučera
Evolutionary Bioinformatics 2010:6 97-112
Original Research | Published on 09 Sep 2010

Molecular Phylogeny of Edge Hill Virus Supports its Position in the Yellow Fever Virus Group and Identifies a New Genetic Variant
Joanne Macdonald, Michael Poidinger, John S. Mackenzie, Richard C. Russell, Stephen Doggett, Annette K. Broom, Debra Phillips, Joseph Potamski, Geoff Gard, Peter Whelan, Richard Weir, Paul R. Young, Debra Gendle, Sheryl Maher, Ross T. Barnard and Roy A. Hall
Evolutionary Bioinformatics 2010:6 91-96
Short Report | Published on 15 Jun 2010

Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference Versus Group-Specific Taxon Sampling
Alexandros Stamatakis, Markus Göker and Guido W. Grimm
Evolutionary Bioinformatics 2010:6 73-90
Original Research | Published on 24 May 2010

An Application of Supertree Methods to Mammalian Mitogenomic Sequences
Véronique Campbell and François-Joseph Lapointe
Evolutionary Bioinformatics 2010:6 57-71
Original Research | Published on 12 May 2010

Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias
Soohyun Lee, Seyeon Weon, Sooncheol Lee and Changwon Kang
Evolutionary Bioinformatics 2010:6 47-55
Original Research | Published on 05 May 2010

A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction
Ra’ed M. Al-Khatib, Rosni Abdullah and Nur’aini Abdul Rashid
Evolutionary Bioinformatics 2010:6 27-45
Original Research | Published on 09 Apr 2010

Comparative Molecular Evolution of Trichoderma Chitinases in Response to Mycoparasitic Interactions
Katarina Ihrmark, Nashwan Asmail, Wimal Ubhayasekera, Petter Melin, Jan Stenlid and Magnus Karlsson
Evolutionary Bioinformatics 2010:6 1-26
Original Research | Published on 15 Mar 2010

Clustering Protein Sequences Using Affinity Propagation Based on an Improved Similarity Measure
Fan Yang, Qing-Xin Zhu, Dong-Ming Tang and Ming-Yuan Zhao
Evolutionary Bioinformatics 2009:5 137-146
Methodology | Published on 22 Jan 2010

Snapshots of Tree Space
Zheng Wang, Francesc López-Giráldez and Jeffrey P. Townsend
Evolutionary Bioinformatics 2009:5 133-136
Short Commentary | Published on 18 Jan 2010

Genome-Wide Identification and Evolutionary Analysis of the Animal Specific ETS Transcription Factor Family
Zhipeng Wang and Qin Zhang
Evolutionary Bioinformatics 2009:5 119-131
Original Research | Published on 02 Oct 2009

A Model for Protein Sequence Evolution Based on Selective Pressure for Protein Stability: Application to Hemoglobins
Lorraine Marsh
Evolutionary Bioinformatics 2009:5 107-118
Original Research | Published on 27 Aug 2009

On the Use of Bootstrapped Topologies in Coalescent-Based Bayesian MCMC Inference: A Comparison of Estimation and Computational Efficiencies
Allen G. Rodrigo, Peter Tsai and Helen Shearman
Evolutionary Bioinformatics 2009:5 97-105
Original Research | Published on 31 Jul 2009

PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics
Robert C. Thomson
Evolutionary Bioinformatics 2009:5 91-95
Short Report | Published on 30 Jul 2009

A Comprehensive Analysis of Gene Expression Evolution Between Humans and Mice
Yupeng Wang and Romdhane Rekaya
Evolutionary Bioinformatics 2009:5 81-90
Original Research | Published on 06 Jul 2009

Initial Implementation of a Comparative Data Analysis Ontology
Francisco Prosdocimi, Brandon Chisham, Enrico Pontelli, Julie D. Thompson and Arlin Stoltzfus
Evolutionary Bioinformatics 2009:5 47-66
Methodology | Published on 03 Jul 2009

A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies
Bastien Boussau, Laurent Guéguen and Manolo Gouy
Evolutionary Bioinformatics 2009:5 67-79
Methodology | Published on 25 Jun 2009

Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters
Marc Thuillard and Didier Fraix-Burnet
Evolutionary Bioinformatics 2009:5 33-46
Original Research | Published on 11 Jun 2009

Phylogenetic Analyses Reveal Monophyletic Origin of the Ergot Alkaloid Gene dmaW in Fungi
Miao Liu, Daniel G. Panaccione and Christopher L. Schardl
Evolutionary Bioinformatics 2009:5 15-30
Original Research | Published on 04 Jun 2009

Evolution and Functional Diversification of the GLI Family of Transcription Factors in Vertebrates
Amir Ali Abbasi, Debbie K. Goode, Saneela Amir and Karl-Heinz Grzeschik
Evolutionary Bioinformatics 2009:5 5-13
Original Research | Published on 18 May 2009

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era
Guy Leonard, Jamie R. Stevens and Thomas A. Richards
Evolutionary Bioinformatics 2009:5 1-4
Short Report | Published on 06 May 2009

The Austronesian Basic Vocabulary Database: From Bioinformatics to Lexomics
Simon J. Greenhill, Robert Blust and Russell D. Gray
Evolutionary Bioinformatics 2008:4 271-283
Published on 03 Nov 2008

Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence
R.S. Ross, J. Verbeeck, S. Viazov, P. Lemey, M. Van Ranst and M. Roggendorf
Evolutionary Bioinformatics 2008:4 249-254
Published on 30 Oct 2008

Inconsistent Distances in Substitution Matrices can be Avoided by Properly Handling Hydrophobic Residues
J. Baussand and A. Carbone
Evolutionary Bioinformatics 2008:4 255-261
Published on 09 Oct 2008

Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers
Haseeb A. Khan, Ibrahim A. Arif, Ali H. Bahkali, Ahmad H. Al Farhan and Ali A. Al Homeidan
Evolutionary Bioinformatics 2008:4 263-270
Published on 06 Oct 2008

Minimum Contradiction Matrices in Whole Genome Phylogenies
Marc Thuillard
Evolutionary Bioinformatics 2008:4 237-247

Published on 21 Jul 2008

Estimation of Genetic Effects and Genotype-Phenotype Maps
Arnaud Le Rouzic and José M. Álvarez-Castro
Evolutionary Bioinformatics 2008:4 225-235
Published on 28 Jun 2008

Testing the Accuracy of Eukaryotic Phylogenetic Profiles for Prediction of Biological Function
Saurav Singh and Dennis P. Wall
Evolutionary Bioinformatics 2008:4 217-223
Published on 18 Jun 2008

Electrostatic and Functional Analysis of the Seven-Bladed WD β-Propellers
Najl V Valeyev, A Kristina Downing, John Sondek and Charlotte Deane
Evolutionary Bioinformatics 2008:4 203-216
Published on 13 Jun 2008

Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification
R. Henrik Nilsson, Erik Kristiansson, Martin Ryberg, Nils Hallenberg and Karl ­Henrik Larsson
Evolutionary Bioinformatics 2008:4 193-201
Published on 26 May 2008

Exploring the Evolutionary History of the Differentially Expressed Genes between Human Populations: Action of Recent Positive Selection
Wei Zhang and M. Eileen Dolan
Evolutionary Bioinformatics 2008:4 171-179
Published on 15 May 2008

Maximum Gene-Support Tree
Yunfeng Shan and Xiu-Qing Li
Evolutionary Bioinformatics 2008:4 181-191
Published on 15 May 2008

Examining Ancient Inter-domain Horizontal Gene Transfer
Francisca C. Almeida, Magdalena Leszczyniecka, Paul B. Fisher and Rob DeSalle
Evolutionary Bioinformatics 2008:4 109-119
Published on 09 May 2008

Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
Anthony Levasseur, Pierre Pontarotti, Olivier Poch and Julie D. Thompson
Evolutionary Bioinformatics 2008:4 121-137
Published on 08 May 2008

Dissection of Functional Residues in Receptor Activity-Modifying Proteins Through Phylogenetic and Statistical Analyses
Alfonso Benítez-Páez and Sonia Cárdenas-Brito
Evolutionary Bioinformatics 2008:4 153-169
Published on 28 Apr 2008

Assessing the Evolution of Gene Expression Using Microarray Data
Owen Z. Woody, Andrew C. Doxey and Brendan J. McConkey
Evolutionary Bioinformatics 2008:4 139-152
Published on 24 Apr 2008

Identifying Coevolving Partners from Paralogous Gene Families
Chen-Hsiang Yeang
Evolutionary Bioinformatics 2008:4 97-107
Published on 24 Apr 2008

The ABCs of MGR with DCJ
Zaky Adam and David Sankoff
Evolutionary Bioinformatics 2008:4 69-74
Published on 10 Apr 2008

Comparative Evolutionary Histories of the Fungal Chitinase Gene Family Reveal Non-Random Size Expansions and Contractions due to Adaptive Natural Selection
Magnus Karlsson and Jan Stenlid
Evolutionary Bioinformatics 2008:4 47-60
Published on 18 Mar 2008

Expected Anomalies in the Fossil Record
Mareike Fischer and Mike Steel
Evolutionary Bioinformatics 2008:4 61-67
Published on 18 Mar 2008

How to Summarize Estimates of Ancestral Divergence Times
David A. Morrison
Evolutionary Bioinformatics 2008:4 75-95
Published on 18 Mar 2008

A Simple Derivation of the Distribution of Pairwise Local Protein Sequence Alignment Scores
Olivier Bastien
Evolutionary Bioinformatics 2008:4 41-45
Published on 14 Feb 2008

Why Should We Care About Molecular Coevolution?
Francisco M. Codoñer and Mario A. Fares
Evolutionary Bioinformatics 2008:4 29-38
Published on 14 Feb 2008

Detecting Microsatellites in Genome Data: Variance in Definitions and Bioinformatic Approaches Cause Systematic Bias
Angelika Merkel and Neil J. Gemmell
Evolutionary Bioinformatics 2008:4 1-6
Published on 09 Feb 2008

Reverse Conservation Analysis Reveals the Specificity Determining Residues of Cytochrome P450 Family 2 (CYP 2)
Tai-Sung Lee
Evolutionary Bioinformatics 2008:4 7-16
Published on 09 Feb 2008

SPR Distance Computation for Unrooted Trees
Glenn Hickey, Frank Dehne, Andrew Rau-Chaplin and Christian Blouin
Evolutionary Bioinformatics 2008:4 17-27
Published on 09 Feb 2008

Evolution of the Influenza A Virus: Some New Advances
Raul Rabadan and Harlan Robins
Evolutionary Bioinformatics Online 2007:3 299-307
Published on 30 Jan 2008